Where to find the latest recommended MAFs for TCGA? particularly after TCGA data has been moved to GDC.
- There are no MAF files on the GDC,
- The NCI wiki lists set of current and obsolete maf files, but the links mentioned are not working now. (Also in archive many files which are listed are not available for e.g. SKCM only one somatic file is present in archive)
I read some of the threads in BioStars which recommend some sources I have questions on these..
- The Ding lab at TGI, WashU track the best available MAFs in this spreadsheet for use in MuSiC analyses.
Q1: The links for these files are no longer working
- For Broad's firehose recommended files,
Q1: Why there are multiple files for certain cancers such as COAD, READ etc??
Q2: The links for these files are no longer working
- Recently, CGC also has a set of recommended files,
Q: The links for these files are no longer working
Among the above three sources which files should be considered for analysis of somatic mutations? For, some cancer types, files are same among three above recommendations. But for cancers like ACC, firehose recommends different file than Ding lab and CGC?
Any directions for using right set of files from TCGA??